Variant report

Variant	rs11681868
Chromosome Location	chr2:48787040-48787041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STON1-1	chr2:48786942-48787278	NONHSAT070624

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11125176	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11676150	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11678306	0.80[EUR][1000 genomes]
rs11681276	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11681426	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11683611	0.80[EUR][1000 genomes]
rs11693429	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11693691	0.80[EUR][1000 genomes]
rs12990079	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12992870	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12999304	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13010692	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13014112	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13016899	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13025488	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13027618	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13030948	0.81[EUR][1000 genomes]
rs13031184	0.82[EUR][1000 genomes]
rs13034063	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13034951	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17039250	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2103112	0.82[EUR][1000 genomes]
rs2177489	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293270	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293271	0.98[ASN][1000 genomes]
rs2293272	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293274	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2349098	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2882084	0.82[EUR][1000 genomes]
rs3749144	0.81[EUR][1000 genomes]
rs3749145	0.82[EUR][1000 genomes]
rs3792234	0.88[ASN][1000 genomes]
rs3792235	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3792236	0.82[EUR][1000 genomes]
rs4566410	0.80[EUR][1000 genomes]
rs4953593	0.86[EUR][1000 genomes]
rs55641971	0.82[EUR][1000 genomes]
rs55700200	0.82[EUR][1000 genomes]
rs56111874	0.82[EUR][1000 genomes]
rs62135201	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62135230	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62135231	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62135232	0.83[EUR][1000 genomes]
rs62135233	0.82[EUR][1000 genomes]
rs62135236	0.82[EUR][1000 genomes]
rs6545048	0.89[ASN][1000 genomes]
rs6709043	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6712592	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6712724	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6722556	0.82[EUR][1000 genomes]
rs6727929	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6729860	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6732365	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6737732	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6741341	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6741677	0.82[EUR][1000 genomes]
rs6757847	0.80[EUR][1000 genomes]
rs940389	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1007491	chr2:48752185-48796441	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv535683	chr2:48752185-48796441	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv581776	chr2:48763382-48913019	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1000419	chr2:48766957-48795327	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11681868	STON1-GTF2A1L	cis	lung	GTEx
rs11681868	STON1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48759000-48787400	Weak transcription	Psoas Muscle	Psoas
2	chr2:48759000-48827600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr2:48759200-48793200	Weak transcription	Fetal Lung	lung
4	chr2:48767200-48807800	Weak transcription	Aorta	Aorta
5	chr2:48768000-48787600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:48768000-48793800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:48772600-48788000	Weak transcription	Lung	lung
8	chr2:48772800-48787400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:48772800-48787600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:48773000-48787200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:48773000-48808800	Weak transcription	Right Ventricle	heart
12	chr2:48773600-48787600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:48775400-48787400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:48775800-48793600	Weak transcription	Placenta	Placenta
15	chr2:48776600-48794000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr2:48777200-48807800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:48779200-48787600	Weak transcription	Esophagus	oesophagus
18	chr2:48779200-48789800	Weak transcription	Ovary	ovary
19	chr2:48779400-48800200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:48780600-48793800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:48781200-48793000	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:48781200-48793800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:48781400-48787400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:48781400-48787600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:48781400-48789800	Weak transcription	Fetal Stomach	stomach
26	chr2:48781800-48787400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:48781800-48789400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:48784000-48787200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:48785400-48788200	Enhancers	Fetal Muscle Leg	muscle
30	chr2:48786000-48787600	Weak transcription	Right Atrium	heart
31	chr2:48786000-48788400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:48786000-48793600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:48786000-48793600	Weak transcription	Fetal Kidney	kidney
34	chr2:48786600-48787200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:48786600-48788400	Enhancers	Brain Cingulate Gyrus	brain
36	chr2:48786800-48788200	Enhancers	Brain Germinal Matrix	brain
37	chr2:48786800-48788400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr2:48786800-48788400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:48786800-48788400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr2:48787000-48787400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:48787000-48788400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:48787000-48788400	Enhancers	Brain Anterior Caudate	brain
43	chr2:48787000-48788600	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr2:48787000-48790000	Weak transcription	Spleen	Spleen

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